[gmx-users] Initial velocity

[Justin Lemkul]

On 5/13/13 1:48 AM, Acoot Brett wrote:
> Dear All,
>
> Will you please explain how the initial velocity may affect the MD results?

We use different initial velocities to improve sampling, i.e. to allow the 
trajectory to evolve in different ways.  In the end, in the limit of infinite 
sampling, the trajectory ensemble averages should be the same.

> What the initial velocity really means?

Just what it claims to be - the initial (first) velocities of each atom.

> How the velocity of the atoms in the protein changes in the MD process?

Please read about MD integration algorithms.

> What is the reasonable scope of the initial velocity?

I don't know what this means.

> Any suggestions on how to manually input a defined initial velocity?

Provide grompp with an input file that has velocities - .trr, .edr, .gro, .cpt.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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